Project Description

In the #sourcecode Project, students were put into groups of 4-5, with the groups named after different Star Wars and then given the tasks of

Writing a computer program that, when a human genome was inputted, would output the ancestry of the individual

Identifying and researching diseases held within the alleles of the individual

Design an infographic that explained both the ancestry and the characteristics of a specific disease held within the genome of the individual whose data we were using

Produce a piece of "Code Art," an artistic representation if our group's Star Wars character using lines from the code we wrote

To familiarize ourselves with computer programming, we all had to complete the Python tutorial on Code Academy, and had various lectures from Computer Science Professors as well as from professional bioinformaticists. As part of this project, we also read The Immortal Life of Henrietta Lacks by Rebecca Skloot. The Immortal Life of Henrietta Lacks tells the story of HeLa cells, the first immortal cell line ever produced in a laboratory, the story of the woman from whom they originated, the state of the Lacks family, and raises several questions about bioethics. The final point about bioethics was especially relevant to our project, as we would be downloading a total stranger's complete genome from the 23andme database.

That genome is the information we inputed into our code, and then compared the output to the 1Kg File, a collection of 1,000 mapped genomes whose ancestry is known. By identifying which similarities our genome contained with other people from the 1Kg File, we were able to determine from what populations our individuals ancestors were from.

Group Role - Biologist

The biologists were responsible for identifying which diseases our subject was a carrier of. We took the output of the code that Matt Schultz wrote for us (since we did not have enough time to write both an ancestry and diseases code), and identified which alleles our subject carried that are associated with certain diseases. Mackenzie, our biology teacher, then filtered out all the diseases that our subject carried that were NOT pathogenic (meaning they are not harmful). That narrowed down the return of the algorithm to around 50 diseases from an original 22,000 returned diseases. The biologists of each group then conducted detailed and specific research on the diseases that they found most interesting from the final 50. Finally, Biologists had to decide which of the various diseases they had researched to include on their groups infographic. Two key clarifications that all biologists are compelled to make are that 1) the diseases we researched are associated with alleles; if you carry the allele it neither means that you suffer from that diseases nor guarantees that you will develop the associated disease, and 2) you can carry the allele with which a certain disease is associated without you or your offsprings ever suffering or obtaining that pathogenic disease (as in the cases of the infographics, each of those diseases is carried by the subject, but it does not mean that the subject is a victim of that disease).

Challenges

This project contained many challenges, as would be expected from a computer programming project. Obviously, the biggest challenge from this project was writing the code. Seriously, no other challenge even came close to writing the computer program. Anyone that has ever coded anything or tried to learn any level of programming can attest to how stressful and frustrating computer programming is (but also how fun it is). To tell a computer what to do, you have to be specific about every single detail; every command, every semi colon, every comma and every dictionary. What I always realized but never really understood until this project is that computers do not think. I had never tried programming a computer prior to this program, and as all of us are so used to interacting with people who actually think you don't realize how much better your brain is than any hard drive out there, because the computer can do virtually nothing for itself.

Other challenges included printing our infographic, and producing our code art. The website we had originally used to produce our infographic caused us a serious heart attack at the end of the project, because it would not let us set our own dimensions for the printing of our infographic. So in the days leading up to exhibition, we had to start from scratch on a new website, and had to cut almost half of the information that our original infographic contained, as well as having to remove all of the illustrations and characters that our original infographic contained. The challenge with the Code Art was finding an image that we could work with. We were making our image with adobe photoshop, and it was very tiring aligning the code, shadowing and coloring that formulated the image intended and not just a bunch of lined gibberish.

Lessons Learned

I think this project provided many lessons that will serve me well after high school. For one, computer programming is a skill that every student of the 21st century should learn, especially those that plan on pursuing careers in any scientific field. For me, currently wanting to pursue a career in Aerospace Engineering or Nuclear Physics, computer programming skills are a must have. What typing used to be, computer programming is now. My parents had to take typing classes when they were in high school and college, and now typing is something that everyone knows. To quote Ashton Kutcher, "Computer sciences belongs in every public school, right next to biology, chemistry, or algebra." Computer programming is not there yet, so knowing how to code puts me a step ahead of my future peers and coworkers that will have to learn how to code on top of everything else. Gaining some understanding of how Photoshop works could also come in handy some time in the future. And of course, familiarizing myself with and developing my own beliefs on the debate known as bioethics is something that I don't think will ever leave me.

Powered by Create your own unique website with customizable templates.